http://www.seocase.net/search-engine-position-checker-msn-ranking.php try this.. it checks msn Uk and MSN world rankings.. they have Yahoo, Google, Ask, Alta vista, Aol also Cheers
Manual checking is always the best for your website. I use softwares to check my competitors ranking.,
http://www.prsearch.biz/msnmass.php this is a good tool to check your site for multiple kws in msn. these results are usually accurate on manual check also. works for me most of the time. yes i agree that it doesnot work very well with yahoo.com